From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Tue, 9 Feb 2016 10:25:14 +0000 (+0000)
Subject: JAL-1957 enabled multi-chain mapping and highlight for Chimera viewer
X-Git-Tag: Release_2_10_0~317
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d787bb9555e6ad57ae4e10a89f842345ff05ec77;p=jalview.git

JAL-1957 enabled multi-chain mapping and highlight for Chimera viewer
---

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index 5342dc8..a551ca2 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -232,7 +232,7 @@ public class ChimeraCommands
               addColourRange(colourMap, lastColour, pdbfnum, startPos,
                       lastPos, lastChain);
             }
-            break;
+            // break;
           }
         }
       }
diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 368918b..cae2457 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -831,6 +831,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     }
     StringBuilder atomSpecs = new StringBuilder();
     boolean first = true;
+
     for (AtomSpec atom : atoms)
     {
       int pdbResNum = atom.getPdbResNum();
@@ -843,9 +844,9 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
          * Formatting as #0:34.A,#1:33.A doesn't work as desired, so instead we
          * concatenate multiple 'show' commands
          */
-        atomSpecs.append(first ? "" : ";show ");
+        atomSpecs.append(first ? "" : ",");
         first = false;
-        atomSpecs.append("#" + cms.get(0).getModelNumber());
+        atomSpecs.append(cms.get(0).getModelNumber());
         atomSpecs.append(":" + pdbResNum);
         if (!chain.equals(" "))
         {
@@ -867,7 +868,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     viewerCommandHistory(false);
     if (atomSpec.length() > 0)
     {
-      command.append("show ").append(atomSpec);
+      command.append("show #").append(atomSpec);
       viewer.sendChimeraCommand(command.toString(), false);
     }
     viewerCommandHistory(true);
@@ -994,6 +995,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public abstract void refreshGUI();
 
+  @Override
   public void setLoadingFromArchive(boolean loadingFromArchive)
   {
     this.loadingFromArchive = loadingFromArchive;
@@ -1004,6 +1006,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * @return true if Chimeral is still restoring state or loading is still going
    *         on (see setFinsihedLoadingFromArchive)
    */
+  @Override
   public boolean isLoadingFromArchive()
   {
     return loadingFromArchive && !loadingFinished;
@@ -1015,6 +1018,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * 
    * @param finishedLoading
    */
+  @Override
   public void setFinishedLoadingFromArchive(boolean finishedLoading)
   {
     loadingFinished = finishedLoading;